The game was developed long before the Wii U even started development. In an Iwata Asks interview, Masataka Takemoto stated that the team used materials from New Super Mario Bros. Wii. By the time the Wii U GamePad was announced, he considered having four-player cooperative play with an extra player using said GamePad to add blocks.

New Super Mario Bros. U began as a tech demo, shown at E3 2011, called New Super Mario Bros. Mii. It allowed players to use Miis in all modes. If all four players chose Miis, Player 1 would be dressed as Mario, Player 2 as Luigi, Player 3 as Wario, and Player 4 as Waluigi but with blue sleeves.

While Miis are no longer selectable in all game modes, this concept did make it to the final game in the form of "Boost Rush Mode".